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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.25

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by:

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2024-11-07, 09:50 CET based on data in: /DKHC/scratch/markop/_p_Endophytes/_I_Bsubtilis/_S_NGS_mixed_cultures_exp2/_A_03_exp2-STAR_limma/output

General Statistics

Showing ⁰/₆₀ rows and ³/₇ columns.

Sample Name	Total reads	Aligned	Aligned	Uniq aligned	Uniq aligned	Multimapped	Trimmed bases
BS830	21.8M	19.9M	91.0%	18.9M	86.7%	0.9M
BS830_1							0.5%
BS830_2							0.6%
BS831	22.2M	20.6M	92.5%	19.7M	88.3%	0.9M
BS831_1							0.5%
BS831_2							0.6%
BS832	21.3M	19.4M	91.1%	18.6M	87.1%	0.9M
BS832_1							0.5%
BS832_2							0.6%
BS833	20.6M	18.9M	91.8%	18.1M	88.0%	0.8M
BS833_1							0.5%
BS833_2							0.6%
BS839	24.2M	21.4M	88.6%	20.3M	83.8%	1.2M
BS839_1							0.6%
BS839_2							0.6%
BS840	20.3M	17.3M	84.9%	16.2M	79.9%	1.0M
BS840_1							0.5%
BS840_2							0.5%
BS847	25.7M	19.9M	77.3%	18.2M	70.5%	1.7M
BS847_1							0.5%
BS847_2							0.5%
BS848	21.4M	19.4M	90.5%	18.5M	86.6%	0.8M
BS848_1							0.5%
BS848_2							0.5%
BS849	21.4M	15.7M	73.2%	14.9M	69.4%	0.8M
BS849_1							0.8%
BS849_2							0.5%
BS855	20.4M	17.3M	85.0%	16.4M	80.6%	0.9M
BS855_1							0.5%
BS855_2							0.5%
BS856	21.6M	19.6M	91.1%	18.8M	87.3%	0.8M
BS856_1							0.4%
BS856_2							0.5%
BS857	21.2M	19.0M	89.5%	18.1M	85.3%	0.9M
BS857_1							0.5%
BS857_2							0.5%
BS862	23.2M	21.0M	90.5%	20.2M	86.9%	0.8M
BS862_1							0.5%
BS862_2							0.5%
BS863	22.6M	18.9M	83.6%	17.7M	78.3%	1.2M
BS863_1							0.5%
BS863_2							0.5%
BS864	24.7M	17.9M	72.5%	17.0M	68.7%	0.9M
BS864_1							0.8%
BS864_2							0.8%
BS865	38.6M	34.2M	88.7%	32.8M	85.0%	1.4M
BS865_1							0.5%
BS865_2							0.5%
BS870	20.2M	18.2M	90.3%	17.4M	86.2%	0.8M
BS870_1							0.5%
BS870_2							0.5%
BS871	25.3M	16.1M	63.7%	15.3M	60.5%	0.8M
BS871_1							0.5%
BS871_2							0.5%
BS872	25.5M	22.2M	86.9%	21.2M	82.9%	1.0M
BS872_1							0.5%
BS872_2							0.5%
BS873	21.8M	18.7M	86.0%	17.8M	81.5%	1.0M
BS873_1							0.5%
BS873_2							0.5%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	STAR	Total reads	Number of input reads	`star-total_reads`	read_count
\|\|	STAR	Aligned	Mapped reads	`star-mapped`	read_count
\|\|	STAR	Aligned	% Mapped reads	`star-mapped_percent`
\|\|	STAR	Uniq aligned	Uniquely mapped reads	`star-uniquely_mapped`	read_count
\|\|	STAR	Uniq aligned	% Uniquely mapped reads	`star-uniquely_mapped_percent`
\|\|	STAR	Multimapped	Multiple mapped reads	`star-multimapped`	read_count
\|\|	Cutadapt	Trimmed bases	% total base pairs trimmed	`cutadapt-percent_trimmed`

STAR

Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

Summary Statistics

Summary statistics from the STAR alignment

Showing ⁰/₂₀ rows and ¹⁰/₁₉ columns.

Sample Name	Total reads	Aligned	Aligned	Uniq aligned	Uniq aligned	Multimapped	Avg. read len	Avg. mapped len	Splices	Annotated splices	GT/AG splices	GC/AG splices	AT/AC splices	Non-canonical splices	Mismatch rate	Del rate	Del len	Ins rate	Ins len
BS830	21.8M	19.9M	91.0%	18.9M	86.7%	0.9M	298.0bp	291.7bp	18.4M	16.6M	18.2M	0.2M	0.0M	0.1M	0.8%	0.1%	3.1bp	0.0%	3.2bp
BS831	22.2M	20.6M	92.5%	19.7M	88.3%	0.9M	298.0bp	291.3bp	18.6M	16.7M	18.3M	0.2M	0.0M	0.1M	0.8%	0.1%	3.1bp	0.1%	3.2bp
BS832	21.3M	19.4M	91.1%	18.6M	87.1%	0.9M	298.0bp	291.6bp	18.4M	16.6M	18.2M	0.2M	0.0M	0.1M	0.8%	0.1%	3.1bp	0.0%	3.2bp
BS833	20.6M	18.9M	91.8%	18.1M	88.0%	0.8M	298.0bp	291.2bp	17.3M	15.6M	17.1M	0.2M	0.0M	0.1M	0.8%	0.1%	3.1bp	0.1%	3.2bp
BS839	24.2M	21.4M	88.6%	20.3M	83.8%	1.2M	298.0bp	290.3bp	16.7M	14.9M	16.5M	0.1M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.5bp
BS840	20.3M	17.3M	84.9%	16.2M	79.9%	1.0M	298.0bp	290.1bp	12.4M	11.0M	12.3M	0.1M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.7bp
BS847	25.7M	19.9M	77.3%	18.2M	70.5%	1.7M	298.0bp	290.6bp	14.5M	12.9M	14.4M	0.1M	0.0M	0.0M	0.8%	0.1%	3.4bp	0.1%	3.7bp
BS848	21.4M	19.4M	90.5%	18.5M	86.6%	0.8M	298.0bp	291.0bp	16.5M	14.7M	16.3M	0.1M	0.0M	0.0M	0.8%	0.1%	3.3bp	0.1%	3.4bp
BS849	21.4M	15.7M	73.2%	14.9M	69.4%	0.8M	298.0bp	291.2bp	13.3M	11.9M	13.1M	0.1M	0.0M	0.0M	0.8%	0.1%	3.2bp	0.1%	3.4bp
BS855	20.4M	17.3M	85.0%	16.4M	80.6%	0.9M	298.0bp	290.2bp	12.8M	11.4M	12.6M	0.1M	0.0M	0.1M	0.9%	0.1%	3.3bp	0.1%	3.5bp
BS856	21.6M	19.6M	91.1%	18.8M	87.3%	0.8M	298.0bp	290.3bp	15.6M	13.9M	15.4M	0.1M	0.0M	0.1M	0.9%	0.1%	3.3bp	0.1%	3.5bp
BS857	21.2M	19.0M	89.5%	18.1M	85.3%	0.9M	298.0bp	290.2bp	14.4M	12.9M	14.2M	0.1M	0.0M	0.1M	0.9%	0.1%	3.3bp	0.1%	3.5bp
BS862	23.2M	21.0M	90.5%	20.2M	86.9%	0.8M	298.0bp	290.5bp	16.5M	14.8M	16.3M	0.1M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.5bp
BS863	22.6M	18.9M	83.6%	17.7M	78.3%	1.2M	298.0bp	290.5bp	14.8M	13.2M	14.6M	0.1M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.5bp
BS864	24.7M	17.9M	72.5%	17.0M	68.7%	0.9M	297.0bp	289.4bp	12.6M	11.2M	12.5M	0.1M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.6bp
BS865	38.6M	34.2M	88.7%	32.8M	85.0%	1.4M	298.0bp	290.7bp	29.8M	26.7M	29.4M	0.3M	0.0M	0.1M	0.8%	0.1%	3.3bp	0.1%	3.3bp
BS870	20.2M	18.2M	90.3%	17.4M	86.2%	0.8M	298.0bp	290.5bp	14.0M	12.5M	13.9M	0.1M	0.0M	0.0M	0.8%	0.1%	3.3bp	0.1%	3.5bp
BS871	25.3M	16.1M	63.7%	15.3M	60.5%	0.8M	298.0bp	290.5bp	12.7M	11.4M	12.5M	0.1M	0.0M	0.0M	0.8%	0.1%	3.4bp	0.1%	3.7bp
BS872	25.5M	22.2M	86.9%	21.2M	82.9%	1.0M	298.0bp	290.6bp	18.0M	16.2M	17.8M	0.1M	0.0M	0.1M	0.8%	0.1%	3.4bp	0.1%	3.5bp
BS873	21.8M	18.7M	86.0%	17.8M	81.5%	1.0M	298.0bp	290.6bp	14.3M	12.9M	14.2M	0.1M	0.0M	0.0M	0.8%	0.1%	3.3bp	0.1%	3.6bp

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: star_summary_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	STAR	Total reads	Number of input reads	`star-total_reads`	read_count
\|\|	STAR	Aligned	Mapped reads	`star-mapped`	read_count
\|\|	STAR	Aligned	% Mapped reads	`star-mapped_percent`
\|\|	STAR	Uniq aligned	Uniquely mapped reads	`star-uniquely_mapped`	read_count
\|\|	STAR	Uniq aligned	% Uniquely mapped reads	`star-uniquely_mapped_percent`
\|\|	STAR	Multimapped	Multiple mapped reads	`star-multimapped`	read_count
\|\|	STAR	Avg. read len	Average input read length	`star-avg_input_read_length`
\|\|	STAR	Avg. mapped len	Average mapped length	`star-avg_mapped_read_length`
\|\|	STAR	Splices	Number of splices: Total	`star-num_splices`	read_count
\|\|	STAR	Annotated splices	Number of splices: Annotated (sjdb)	`star-num_annotated_splices`	read_count
\|\|	STAR	GT/AG splices	Number of splices: GT/AG	`star-num_GTAG_splices`	read_count
\|\|	STAR	GC/AG splices	Number of splices: GC/AG	`star-num_GCAG_splices`	read_count
\|\|	STAR	AT/AC splices	Number of splices: AT/AC	`star-num_ATAC_splices`	read_count
\|\|	STAR	Non-canonical splices	Number of splices: Non-canonical	`star-num_noncanonical_splices`	read_count
\|\|	STAR	Mismatch rate	Mismatch rate per base	`star-mismatch_rate`
\|\|	STAR	Del rate	Deletion rate per base	`star-deletion_rate`
\|\|	STAR	Del len	Deletion average length	`star-deletion_length`
\|\|	STAR	Ins rate	Insertion rate per base	`star-insertion_rate`
\|\|	STAR	Ins len	Insertion average length	`star-insertion_length`

Alignment Scores

Created with MultiQC

Gene Counts

Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

Created with MultiQC

Cutadapt

Version:


                      
                        2.10

Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

Filtered Reads

This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

Created with MultiQC

Trimmed Sequence Lengths (3')

This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
Cutadapt	`2.10`

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General Statistics

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STAR

Summary Statistics

STAR: Summary Statistics: Columns

Alignment Scores

Gene Counts

Cutadapt

Filtered Reads

Trimmed Sequence Lengths (3') Help

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Trimmed Sequence Lengths (3')